- using R Under development (unstable) (2023-03-19 r84006)
- using platform: x86_64-pc-linux-gnu (64-bit)
- R was compiled by
Debian clang version 15.0.6
GNU Fortran (Debian 12.2.0-14) 12.2.0
- running under: Debian GNU/Linux bookworm/sid
- using session charset: UTF-8
- checking for file ‘stars/DESCRIPTION’ ... OK
- this is package ‘stars’ version ‘0.6-0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘starsdata’
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘stars’ can be installed ... OK
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [2s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
- checking loading without being on the library search path ... [2s/2s] OK
- checking startup messages can be suppressed ... [2s/3s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [48s/62s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [34s/44s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
read_ncdf 6.115 0.075 8.217
st_apply 4.852 0.079 5.597
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [138s/174s] ERROR
Running ‘aggregate.R’ [5s/6s]
Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4
< Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE
---
> Linking to GEOS 3.9.3, GDAL 3.5.2, PROJ 8.2.1; sf_use_s2() is TRUE
Running ‘align.R’ [3s/4s]
Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK
Running ‘area.R’ [3s/3s]
Comparing ‘area.Rout’ to ‘area.Rout.save’ ...51a52,64
> /PRODUCT/longitude,
> /PRODUCT/latitude,
> /PRODUCT/SUPPORT_DATA/DETAILED_RESULTS/nitrogendioxide_summed_total_column,
> stars object with 2 dimensions and 1 attribute
> attribute(s):
> Min. 1st Qu. Median Mean 3rd Qu. Max.
> area [m^2] 64503163 64957713 65834712 65849060 66734597 67218777
> dimension(s):
> from to refsys values x/y
> x 1 5 WGS 84 [5x5] -5.81066 [°],...,-5.26234 [°] [x]
> y 1 5 WGS 84 [5x5] 44.4439 [°],...,44.8693 [°] [y]
> curvilinear grid
> There were 15 warnings (use warnings() to see them)
Running ‘crop.R’ [5s/6s]
Comparing ‘crop.Rout’ to ‘crop.Rout.save’ ... OK
Running ‘curvilinear.R’ [2s/3s]
Comparing ‘curvilinear.Rout’ to ‘curvilinear.Rout.save’ ...54a55,70
> /PRODUCT/longitude,
> /PRODUCT/latitude,
> /PRODUCT/SUPPORT_DATA/DETAILED_RESULTS/nitrogendioxide_summed_total_column,
> stars object with 3 dimensions and 1 attribute
> attribute(s):
> Min. 1st Qu. Median
> nitrogendioxide_summed_total_c... 3.650813e-05 7.451281e-05 8.296968e-05
> Mean 3rd Qu. Max. NA's
> nitrogendioxide_summed_total_c... 8.581399e-05 9.397442e-05 0.0004535302 330
> dimension(s):
> from to refsys values x/y
> x 1 450 WGS 84 [450x278] -5.81066 [°],...,30.9468 [°] [x]
> y 1 278 WGS 84 [450x278] 28.3605 [°],...,51.4686 [°] [y]
> time 1 1 NA NULL
> curvilinear grid
> There were 15 warnings (use warnings() to see them)
Running ‘datasets.R’ [3s/3s]
Comparing ‘datasets.Rout’ to ‘datasets.Rout.save’ ...29a30,38
> stars_proxy object with 1 attribute in 1 file(s):
> $`MTD_MSIL1C.xml:10m:EPSG_32632`
> [1] "[...]/MTD_MSIL1C.xml:10m:EPSG_32632"
>
> dimension(s):
> from to offset delta refsys values x/y
> x 1 10980 3e+05 10 WGS 84 / UTM zone 32N NULL [x]
> y 1 10980 6e+06 -10 WGS 84 / UTM zone 32N NULL [y]
> band 1 4 NA NA NA B4,...,B8
Running ‘dimensions.R’ [4s/5s]
Comparing ‘dimensions.Rout’ to ‘dimensions.Rout.save’ ... OK
Running ‘ee.R’ [3s/3s]
Comparing ‘ee.Rout’ to ‘ee.Rout.save’ ...6c6
< Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE
---
> Linking to GEOS 3.9.3, GDAL 3.5.2, PROJ 8.2.1; sf_use_s2() is TRUE
Running ‘extract.R’ [3s/3s]
Comparing ‘extract.Rout’ to ‘extract.Rout.save’ ... OK
Running ‘gridtypes.R’ [3s/3s]
Comparing ‘gridtypes.Rout’ to ‘gridtypes.Rout.save’ ... OK
Running ‘nc.R’ [4s/5s]
Comparing ‘nc.Rout’ to ‘nc.Rout.save’ ... OK
Running ‘plot.R’ [5s/5s]
Comparing ‘plot.Rout’ to ‘plot.Rout.save’ ... OK
Running ‘predict.R’ [7s/8s]
Comparing ‘predict.Rout’ to ‘predict.Rout.save’ ... OK
Running ‘proxy.R’ [5s/6s]
Comparing ‘proxy.Rout’ to ‘proxy.Rout.save’ ... OK
Running ‘raster.R’ [15s/18s]
Comparing ‘raster.Rout’ to ‘raster.Rout.save’ ...24c24
< terra 1.7.18
---
> terra 1.6.41
Running ‘rasterize.R’ [5s/6s]
Comparing ‘rasterize.Rout’ to ‘rasterize.Rout.save’ ... OK
Running ‘rectilinear.R’ [3s/5s]
Comparing ‘rectilinear.Rout’ to ‘rectilinear.Rout.save’ ... OK
Running ‘redimension.R’ [3s/3s]
Comparing ‘redimension.Rout’ to ‘redimension.Rout.save’ ... OK
Running ‘sf.R’ [3s/4s]
Comparing ‘sf.Rout’ to ‘sf.Rout.save’ ... OK
Running ‘sp.R’ [3s/4s]
Comparing ‘sp.Rout’ to ‘sp.Rout.save’ ... OK
Running ‘spacetime.R’ [4s/5s]
Running ‘spatstat.R’ [5s/7s]
Comparing ‘spatstat.Rout’ to ‘spatstat.Rout.save’ ...14c14
< spatstat.geom 3.1-0
---
> spatstat.geom 3.0-3
Running ‘stars.R’ [12s/14s]
Comparing ‘stars.Rout’ to ‘stars.Rout.save’ ...212c212
< 4 1841004 1143985
---
> 4 1841005 1143985
216c216
< 8 1841010 1143965
---
> 8 1841011 1143965
Running ‘subset.R’ [3s/4s]
Comparing ‘subset.Rout’ to ‘subset.Rout.save’ ... OK
Running ‘testthat.R’ [18s/21s]
Comparing ‘testthat.Rout’ to ‘testthat.Rout.save’ ... OK
Running ‘tidy.R’ [3s/4s]
Comparing ‘tidy.Rout’ to ‘tidy.Rout.save’ ... OK
Running ‘transform.R’ [3s/4s]
Comparing ‘transform.Rout’ to ‘transform.Rout.save’ ...4a5,9
> Warning messages:
> 1: In fun(libname, pkgname) :
> GEOS versions differ: lwgeom has 3.9.1 sf has 3.9.3
> 2: In fun(libname, pkgname) :
> PROJ versions differ: lwgeom has 7.2.1 sf has 8.2.1
Running ‘warp.R’ [3s/4s]
Comparing ‘warp.Rout’ to ‘warp.Rout.save’ ... OK
Running ‘write.R’ [3s/4s]
Comparing ‘write.Rout’ to ‘write.Rout.save’ ... OK
Running the tests in ‘tests/spacetime.R’ failed.
Complete output:
> suppressPackageStartupMessages(library(stars))
> if (require(spacetime, quietly = TRUE)) {
+ set.seed(1331)
+ Sys.setenv(TZ="UTC")
+ example(STFDF)
+
+ x = st_as_stars(stfdf)
+ xx = as(x, "STFDF")
+
+ # as.xts.stars:
+ library(xts)
+ xts = as.xts(x)
+ st_as_stars(xts)
+ st_as_stars(xts, dimensions = st_dimensions(x))
+
+ library(sp)
+ pts = SpatialPoints(rbind(c(0,0), c(0,1), c(1,0), c(1,1)))
+ gridded(pts) = TRUE
+
+ tm = xts(1:10, as.Date("2010-01-01")+0:9)
+ stfdf = STFDF(pts, tm, data.frame(foo = seq_len(length(pts) * length(tm))))
+ x = st_as_stars(stfdf)
+ xx = as(x, "STFDF")
+
+ x = st_as_stars(as(stfdf, "STSDF"))
+ }
STFDF> sp = cbind(x = c(0,0,1), y = c(0,1,1))
STFDF> row.names(sp) = paste("point", 1:nrow(sp), sep="")
STFDF> library(sp)
STFDF> sp = SpatialPoints(sp)
STFDF> time = as.POSIXct("2010-08-05")+3600*(10:13)
STFDF> m = c(10,20,30) # means for each of the 3 point locations
STFDF> mydata = rnorm(length(sp)*length(time),mean=rep(m, 4))
STFDF> IDs = paste("ID",1:length(mydata))
STFDF> mydata = data.frame(values = signif(mydata,3), ID=IDs)
STFDF> stfdf = STFDF(sp, time, mydata)
STFDF> stfdf
An object of class "STFDF"
Slot "data":
values ID
1 9.38 ID 1
2 21.10 ID 2
3 29.80 ID 3
4 11.50 ID 4
5 19.80 ID 5
6 31.20 ID 6
7 10.40 ID 7
8 20.50 ID 8
9 29.80 ID 9
10 10.30 ID 10
11 21.40 ID 11
12 29.40 ID 12
Slot "sp":
SpatialPoints:
x y
point1 0 0
point2 0 1
point3 1 1
Coordinate Reference System (CRS) arguments: NA
Slot "time":
timeIndex
2010-08-05 10:00:00 1
2010-08-05 11:00:00 2
2010-08-05 12:00:00 3
2010-08-05 13:00:00 4
Slot "endTime":
[1] "2010-08-05 11:00:00 UTC" "2010-08-05 12:00:00 UTC"
[3] "2010-08-05 13:00:00 UTC" "2010-08-05 14:00:00 UTC"
STFDF> stfdf[1:2,]
An object of class "STFDF"
Slot "data":
values ID
1 9.38 ID 1
2 21.10 ID 2
3 11.50 ID 4
4 19.80 ID 5
5 10.40 ID 7
6 20.50 ID 8
7 10.30 ID 10
8 21.40 ID 11
Slot "sp":
SpatialPoints:
x y
point1 0 0
point2 0 1
Coordinate Reference System (CRS) arguments: NA
Slot "time":
timeIndex
2010-08-05 10:00:00 1
2010-08-05 11:00:00 2
2010-08-05 12:00:00 3
2010-08-05 13:00:00 4
Slot "endTime":
[1] "2010-08-05 11:00:00 UTC" "2010-08-05 12:00:00 UTC"
[3] "2010-08-05 13:00:00 UTC" "2010-08-05 14:00:00 UTC"
STFDF> stfdf[,1:2]
An object of class "STFDF"
Slot "data":
values ID
1 9.38 ID 1
2 21.10 ID 2
3 29.80 ID 3
4 11.50 ID 4
5 19.80 ID 5
6 31.20 ID 6
Slot "sp":
SpatialPoints:
x y
point1 0 0
point2 0 1
point3 1 1
Coordinate Reference System (CRS) arguments: NA
Slot "time":
timeIndex
2010-08-05 10:00:00 1
2010-08-05 11:00:00 2
Slot "endTime":
[1] "2010-08-05 11:00:00 UTC" "2010-08-05 12:00:00 UTC"
STFDF> stfdf[,,2]
An object of class "STFDF"
Slot "data":
ID
1 ID 1
2 ID 2
3 ID 3
4 ID 4
5 ID 5
6 ID 6
7 ID 7
8 ID 8
9 ID 9
10 ID 10
11 ID 11
12 ID 12
Slot "sp":
SpatialPoints:
x y
point1 0 0
point2 0 1
point3 1 1
Coordinate Reference System (CRS) arguments: NA
Slot "time":
timeIndex
2010-08-05 10:00:00 1
2010-08-05 11:00:00 2
2010-08-05 12:00:00 3
2010-08-05 13:00:00 4
Slot "endTime":
[1] "2010-08-05 11:00:00 UTC" "2010-08-05 12:00:00 UTC"
[3] "2010-08-05 13:00:00 UTC" "2010-08-05 14:00:00 UTC"
STFDF> stfdf[,,"values"]
An object of class "STFDF"
Slot "data":
values
1 9.38
2 21.10
3 29.80
4 11.50
5 19.80
6 31.20
7 10.40
8 20.50
9 29.80
10 10.30
11 21.40
12 29.40
Slot "sp":
SpatialPoints:
x y
point1 0 0
point2 0 1
point3 1 1
Coordinate Reference System (CRS) arguments: NA
Slot "time":
timeIndex
2010-08-05 10:00:00 1
2010-08-05 11:00:00 2
2010-08-05 12:00:00 3
2010-08-05 13:00:00 4
Slot "endTime":
[1] "2010-08-05 11:00:00 UTC" "2010-08-05 12:00:00 UTC"
[3] "2010-08-05 13:00:00 UTC" "2010-08-05 14:00:00 UTC"
STFDF> stfdf[1,]
values ID timeIndex
2010-08-05 10:00:00 9.38 ID 1 1
2010-08-05 11:00:00 11.50 ID 4 2
2010-08-05 12:00:00 10.40 ID 7 3
2010-08-05 13:00:00 10.30 ID 10 4
STFDF> stfdf[,2]
coordinates values ID
1 (0, 0) 11.5 ID 4
2 (0, 1) 19.8 ID 5
3 (1, 1) 31.2 ID 6
STFDF> as(stfdf[,,1], "xts")
point1 point2 point3
2010-08-05 10:00:00 9.38 21.1 29.8
2010-08-05 11:00:00 11.50 19.8 31.2
2010-08-05 12:00:00 10.40 20.5 29.8
2010-08-05 13:00:00 10.30 21.4 29.4
STFDF> as(stfdf[,,2], "xts")
point1 point2 point3
2010-08-05 10:00:00 ID 1 ID 2 ID 3
2010-08-05 11:00:00 ID 4 ID 5 ID 6
2010-08-05 12:00:00 ID 7 ID 8 ID 9
2010-08-05 13:00:00 ID 10 ID 11 ID 12
STFDF> # examples for [[, [[<-, $ and $<-
STFDF> stfdf[[1]]
[1] 9.38 21.10 29.80 11.50 19.80 31.20 10.40 20.50 29.80 10.30 21.40 29.40
STFDF> stfdf[["values"]]
[1] 9.38 21.10 29.80 11.50 19.80 31.20 10.40 20.50 29.80 10.30 21.40 29.40
STFDF> stfdf[["newVal"]] <- rnorm(12)
STFDF> stfdf$ID
[1] "ID 1" "ID 2" "ID 3" "ID 4" "ID 5" "ID 6" "ID 7" "ID 8" "ID 9"
[10] "ID 10" "ID 11" "ID 12"
STFDF> stfdf$ID = paste("OldIDs", 1:12, sep="")
STFDF> stfdf$NewID = paste("NewIDs", 12:1, sep="")
STFDF> stfdf
An object of class "STFDF"
Slot "data":
values ID newVal NewID
1 9.38 OldIDs1 -0.3125824 NewIDs12
2 21.10 OldIDs2 -1.0536246 NewIDs11
3 29.80 OldIDs3 -0.7188880 NewIDs10
4 11.50 OldIDs4 -1.0525404 NewIDs9
5 19.80 OldIDs5 -0.8441413 NewIDs8
6 31.20 OldIDs6 1.1420848 NewIDs7
7 10.40 OldIDs7 1.9479070 NewIDs6
8 20.50 OldIDs8 -0.4512836 NewIDs5
9 29.80 OldIDs9 0.6695716 NewIDs4
10 10.30 OldIDs10 0.1269003 NewIDs3
11 21.40 OldIDs11 -0.7273297 NewIDs2
12 29.40 OldIDs12 -0.8151803 NewIDs1
Slot "sp":
SpatialPoints:
x y
point1 0 0
point2 0 1
point3 1 1
Coordinate Reference System (CRS) arguments: NA
Slot "time":
timeIndex
2010-08-05 10:00:00 1
2010-08-05 11:00:00 2
2010-08-05 12:00:00 3
2010-08-05 13:00:00 4
Slot "endTime":
[1] "2010-08-05 11:00:00 UTC" "2010-08-05 12:00:00 UTC"
[3] "2010-08-05 13:00:00 UTC" "2010-08-05 14:00:00 UTC"
STFDF> x = stfdf[stfdf[1:2,],]
Error in .local(from, to, ...) : DLL requires the use of native symbols
Calls: example ... .local -> which_nearest -> which_nearest -> .local -> .Call
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [68s/91s] OK
- checking PDF version of manual ... [8s/12s] OK
- checking HTML version of manual ... [3s/6s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE